Multi-omics Analysis of CRISPRi-Knockdowns Identifies Mechanisms that Buffer Decreases of Enzymes in E. coli Metabolism

Allosteric Feedback Inhibition Enables Robust Amino Acid Biosynthesis in E. coli by Enforcing Enzyme Overabundance

(2019) Timur Sander et al.   Cell Systems

Time-resolved imaging-based CRISPRi screening

(2019) Daniel Camsund et al.   NATURE METHODS

Genomic organization underlying deletional robustness in bacterial metabolic systems

(2018) Sayed-Rzgar Hosseini et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Four Key Steps Control Glycolytic Flux in Mammalian Cells

(2018) Lukas Bahati Tanner et al.   Cell Systems

Reserve Flux Capacity in the Pentose Phosphate Pathway Enables Escherichia coli 's Rapid Response to Oxidative Stress

(2018) Dimitris Christodoulou et al.   Cell Systems

Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism

(2018) Douglas McCloskey et al.   Nature Communications

Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome

(2018) Douglas McCloskey et al.   Frontiers in Microbiology

Machine Learning Predicts the Yeast Metabolome from the Quantitative Proteome of Kinase Knockouts

(2018) Aleksej Zelezniak et al.   Cell Systems

Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors

(2018) François Rousset et al.   PLoS Genetics

Genomewide landscape of gene–metabolome associations in Escherichia coli

(2017) Tobias Fuhrer et al.   Molecular Systems Biology

In situ genotyping of a pooled strain library after characterizing complex phenotypes

(2017) Michael J Lawson et al.   Molecular Systems Biology

A global resource allocation strategy governs growth transition kinetics of Escherichia coli

(2017) David W. Erickson et al.   NATURE

iML1515, a knowledgebase that computes Escherichia coli traits

(2017) Jonathan M Monk et al.   NATURE BIOTECHNOLOGY

Kinetics of dCas9 target search inEscherichia coli

(2017) Daniel Lawson Jones et al.   SCIENCE

Optimality and sub-optimality in a bacterial growth law

(2017) Benjamin D. Towbin et al.   Nature Communications

Functional Metabolomics Describes the Yeast Biosynthetic Regulome

(2016) Michael Mülleder et al.   CELL

A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria

(2016) Jason M. Peters et al.   CELL

Massively Parallel Interrogation of the Effects of Gene Expression Levels on Fitness

(2016) Leeat Keren et al.   CELL

Metabolite concentrations, fluxes and free energies imply efficient enzyme usage

(2016) Junyoung O Park et al.   Nature Chemical Biology

Systems-level analysis of mechanisms regulating yeast metabolic flux

(2016) S. R. Hackett et al.   SCIENCE

Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments

(2016) Edward J. O’Brien et al.   PLoS Computational Biology

Selection on noise constrains variation in a eukaryotic promoter

(2015) Brian P. H. Metzger et al.   NATURE

Overflow metabolism in Escherichia coli results from efficient proteome allocation

(2015) Markus Basan et al.   NATURE

The quantitative and condition-dependent Escherichia coli proteome

(2015) Alexander Schmidt et al.   NATURE BIOTECHNOLOGY

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

(2015) Zachary A. King et al.   NUCLEIC ACIDS RESEARCH

Pseudo-transition Analysis Identifies the Key Regulators of Dynamic Metabolic Adaptations from Steady-State Data

(2015) Luca Gerosa et al.   Cell Systems

Large-Scale Genetic Perturbations Reveal Regulatory Networks and an Abundance of Gene-Specific Repressors

(2014) Patrick Kemmeren et al.   CELL

Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources

(2014) Gene-Wei Li et al.   CELL

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

(2013) Lei S. Qi et al.   CELL

Promoters maintain their relative activity levels under different growth conditions

(2013) L. Keren et al.   Molecular Systems Biology

Dissecting specific and global transcriptional regulation of bacterial gene expression

(2013) L. Gerosa et al.   Molecular Systems Biology

Pyrimidine homeostasis is accomplished by directed overflow metabolism

(2013) Marshall Louis Reaves et al.   NATURE

Coordination of bacterial proteome with metabolism by cyclic AMP signalling

(2013) Conghui You et al.   NATURE

Synthesis and biological evaluation of flexible and conformationally constrained LpxC inhibitors

(2013) Marius Löppenberg et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Glycolytic strategy as a tradeoff between energy yield and protein cost

(2013) A. Flamholz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global Network Reorganization During Dynamic Adaptations of Bacillus subtilis Metabolism

(2012) J. M. Buescher et al.   SCIENCE

Glycolytic Oscillations and Limits on Robust Efficiency

(2011) F. A. Chandra et al.   SCIENCE

Tradeoff between enzyme and metabolite efficiency maintains metabolic homeostasis upon perturbations in enzyme capacity

(2010) Sarah-Maria Fendt et al.   Molecular Systems Biology

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

(2010) Y. Taniguchi et al.   SCIENCE

Interdependence of Cell Growth and Gene Expression: Origins and Consequences

(2010) M. Scott et al.   SCIENCE

Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli

(2009) Bryson D Bennett et al.   Nature Chemical Biology

Ensemble Modeling of Metabolic Networks

(2008) Linh M. Tran et al.   BIOPHYSICAL JOURNAL